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1,000 results • Page
4 of 20
Sort: replies
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Views
Votes
Replies
4
votes
16
replies
1.0k
views
hisat2 location does not exist
hisat2
updated 9 weeks ago by
Ram
43k • written 10 weeks ago by
Eric
• 0
5
votes
16
replies
2.7k
views
How to extract intron counts from total RNA Sequencing?
featurecounts
RNAseq
htseq
STAR
17 months ago by
PK
▴ 130
0
votes
16
replies
2.8k
views
How to convert ncbi gff file to ensembl gff format
bcftools
gff
updated 13 months ago by
Ram
43k • written 20 months ago by
yoser4
▴ 10
3
votes
16
replies
1.6k
views
Problem, getting information only from the last row and not from all the rows
perl
6.0 years ago by
ArusjakGevorgyan
▴ 30
7
votes
16
replies
3.6k
views
How do I get a GFF file
snp
4.9 years ago by
apl00028
▴ 90
0
votes
16
replies
4.6k
views
Issue using MaSuRCA-3.2.6
Assembly
assembler
updated 5.7 years ago by
Biostar
20 • written 5.9 years ago by
Chvatil
▴ 130
3
votes
16
replies
1.5k
views
How to bring all reads to the same length? Any tool?
Read-length
Bed
updated 10 months ago by
Ram
43k • written 4.3 years ago by
Ankit
▴ 500
3
votes
16
replies
3.5k
views
FastTree trifurcating Root node
alignment
FastTree
Phylogenetic Tree
5.3 years ago by
Moses
▴ 150
9
votes
16
replies
1.5k
views
I am trying to select some reference genome region of a bam file, but got an error
SAMTOOLS
updated 3.7 years ago by
lieven.sterck
15k • written 3.7 years ago by
schlogl
▴ 160
2
votes
16
replies
3.1k
views
Enhancing draft genome using 10X data
10X
draft_genome
Assembly
5.7 years ago by
Mostafa
▴ 20
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 11 months ago by
Ram
43k • written 5.1 years ago by
Star
▴ 60
8
votes
16
replies
1.4k
views
what is the ideal normalistation methods for TCGA gene expression or DNA methylation dtasets?
gene
next-gen
4.3 years ago by
Chaimaa
▴ 260
9
votes
16
replies
1.9k
views
feature extraction from SNPs in R
R
gene
sequence
SNP
5.5 years ago by
bioinfo456
▴ 150
2
votes
16
replies
10k
views
Tophat with Bowtie2 long index
tophat
bowtie
updated 2.3 years ago by
Ram
43k • written 9.8 years ago by
BDK_compbio
▴ 140
5
votes
16
replies
2.6k
views
a lot of OTUs wth no reference
16S
6.5 years ago by
agata88
▴ 870
9
votes
16
replies
3.8k
views
6 follow
covert SAM to full length fasta
fasta
SAM
updated 13 months ago by
Ram
43k • written 5.7 years ago by
marongiu.luigi
▴ 710
7
votes
16
replies
3.9k
views
cutting overrepresented sequences (recognized by fatsqc)
sequencing
genome-sequence
fastqc
genome
sequence
4.1 years ago by
Researcher
▴ 20
0
votes
16
replies
5.2k
views
Unable To Delete Tmp Files Of Samtools Sort
samtools
sort
11.0 years ago by
chentong.biology
▴ 50
4
votes
16
replies
1.8k
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools
RNAseq
samtools
BAM
updated 10 weeks ago by
Ram
43k • written 7 months ago by
ella
• 0
1
vote
16
replies
2.0k
views
Why I see very high mapping percentage, Is this normal or anything wrong in generating libraries?
RNA-Seq
hisat2
samtools
mapping
updated 5.9 years ago by
Biostar
20 • written 6.0 years ago by
Vasu
▴ 770
0
votes
16
replies
3.8k
views
Gff to genbank - feature is missing
DNA
augustus
gff3
genbank
updated 11 months ago by
Ram
43k • written 5.9 years ago by
rororo
▴ 10
3
votes
16
replies
4.1k
views
GC content of 10x Genomics
fastqc
10x
GC content
updated 3.7 years ago by
Eugene A
▴ 180 • written 5.1 years ago by
Assa Yeroslaviz
★ 1.8k
13
votes
16
replies
7.3k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa
samtools
mpileup
5.3 years ago by
DNAngel
▴ 250
4
votes
16
replies
6.1k
views
How to count occurrence of numbers in text files using phython
python
excel
counting
writelines
7.3 years ago by
Kachibunny
• 0
14
votes
16
replies
2.0k
views
Why are some mapped reads not mapped completely?
RNA-Seq
mapping
updated 3.5 years ago by
lieven.sterck
15k • written 3.5 years ago by
utsafar
▴ 80
4
votes
16
replies
8.7k
views
STAR - genome indexes generation, genome file not created
RNA-Seq
star
updated 4.7 years ago by
Biostar
20 • written 7.5 years ago by
lu.ne
▴ 70
7
votes
16
replies
21k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq
rna-seq
7.8 years ago by
aggregatibacter
▴ 180
4
votes
16
replies
4.5k
views
Working with human database in Kraken
RNA-Seq
next-gen
genome
7.9 years ago by
Ron
★ 1.2k
5
votes
15
replies
2.2k
views
Is this a valid analysis?
geo
rankprod
analysis
microarray
7.5 years ago by
randalljellis
▴ 90
1
vote
15
replies
1.6k
views
Single Cell RNA Seq
scTransform
Harmony
scRNAseq
Seurat
8 months ago by
scRNA2023
• 0
2
votes
15
replies
1.6k
views
How to call all the allele in samples
SNP
6.0 years ago by
Kritika
▴ 260
20
votes
15
replies
30k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 21 months ago by
Ram
43k • written 8.3 years ago by
dam4l
▴ 200
2
votes
15
replies
1.6k
views
from protein to tRNA combinations
RNA-Seq
rna-seq
written 3.4 years ago by
shiningsky000
• 0
6
votes
15
replies
2.7k
views
Why can't I reproduce the same heat map
ggplots
R
RNA-Seq
updated 5.7 years ago by
Biostar
20 • written 5.8 years ago by
Za
▴ 140
7
votes
15
replies
2.2k
views
very low coverage when mappin genomic DNA
mapping
coverage
DNA
genomic
updated 2.7 years ago by
ATpoint
82k • written 2.7 years ago by
Lila M
★ 1.2k
5
votes
15
replies
1.9k
views
Testing uniform distribution of SNPs across chromosome
uniform
vcf
SNP
5.0 years ago by
misterie
▴ 110
6
votes
15
replies
1.6k
views
The Best Cloud Solution For Genomics
cloud
data-sharing
genomics
workflow
updated 21 months ago by
Ram
43k • written 22 months ago by
davidmaimoun
▴ 50
1
vote
15
replies
3.7k
views
Install Lefse in Ubuntu 12
install
lefse
microbiome
5.9 years ago by
goh
▴ 10
0
votes
15
replies
2.2k
views
Chromosome accession numbers correspond to which chromosome?
bam
chromosome
bed
18 months ago by
amy__
▴ 160
0
votes
15
replies
3.7k
views
Identify genes in a tophat aligned bam/sam file
blast
alignment
rna-seq
gene
updated 16 months ago by
Ram
43k • written 8.9 years ago by
gchaves
• 0
3
votes
15
replies
5.6k
views
Pairwise sequence alignment with Biojava?
sequence-alignment
biojava
java
updated 2.3 years ago by
Ram
43k • written 9.5 years ago by
Bioaln
▴ 360
2
votes
15
replies
1.1k
views
Manipulate refseq database
ncbi
database
nt
refseq
updated 4.2 years ago by
Biostar
20 • written 4.3 years ago by
anasofiamoreira94
▴ 80
11
votes
15
replies
2.8k
views
How do I get the read counts for a specific exon
bam
exon
updated 6.1 years ago by
Ram
43k • written 6.1 years ago by
b10hazard
▴ 30
0
votes
15
replies
2.6k
views
Strategy for generating a consensus sequence for 100 complete bacterial genomes?
consensus seq
mauve
5.9 years ago by
Alec Watanabe
▴ 60
4
votes
15
replies
3.3k
views
Adding Multiple readgroups to BAM file
GATK
ReadGroups
8.1 years ago by
vakul.mohanty
▴ 270
1
vote
15
replies
2.8k
views
Copy Number Analysis on single file
CNV
updated 4.7 years ago by
Kevin Blighe
87k • written 4.7 years ago by
user31888
▴ 130
1
vote
15
replies
6.0k
views
How to Extract Specific Region on Bam file
Nanopore
HG38
Rna-Seq
Genome
updated 2.9 years ago by
Kevin Blighe
87k • written 2.9 years ago by
santos48
▴ 40
4
votes
15
replies
4.0k
views
Paired-read alignment length from BAM/SAM file
bam
sam
paired-read
alignment
6.9 years ago by
Soumitra Pal
▴ 10
5
votes
15
replies
1.6k
views
NGS Sequencing depths
next-gen
sequencing
gene
7.2 years ago by
sliproach
▴ 10
3
votes
15
replies
3.2k
views
Less and less genes predicted with each iteration of SNAP/MAKER
maker
annotation
snap
gene prediction
genomics
updated 2.6 years ago by
jaredbernard
▴ 20 • written 4.1 years ago by
mrmrwinter
▴ 30
1,000 results • Page
4 of 20
Recent Votes
Answer: Analysis of intronic reads included scRNA-seq data
Answer: Controlling for FDR in 450k methylation microarray data
Comment: Generating mpileup file using samtools
Comment: Generating mpileup file using samtools
Answer: Downsampling long-read BAM files
Comment: Generating mpileup file using samtools
Answer: What analysis suitable to identify similarly expressed genes between two samples
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Recent Replies
Comment: Generating mpileup file using samtools
by
Ruqaiya
• 0
I didn't use the same tool as in the paper...
Comment: read length in structural variant calling
by
eebloom
▴ 80
Yes good idea. I guess the quality of the SV calls and as a proxy for quality the length and distribution of variants called might be infor…
Comment: Generating mpileup file using samtools
by
Ruqaiya
• 0
I just realised I didn't align my reads with the tools they used and used bowtie2 instead. The tool isn't available on conda and I can't fi…
Comment: Downsampling long-read BAM files
by
eebloom
▴ 80
This is not what I needed for this particular use case, as capping the coverage would lose the information on regions of copy number amplif…
Comment: Do I need to go back and filter my long-reads?
by
eebloom
▴ 80
Apologies, I deleted the question as I wasn't sure it would be helpful to others and it didn't seem to have a clear answer, not to snub the…
Comment: Do I need to go back and filter my long-reads?
by
eebloom
▴ 80
Thanks, I think it would be a good idea to track the results downstream to look for batch effects. I think I will filter the reads ultimate…
Comment: Generating mpileup file using samtools
by
ATpoint
82k
Seconding this. Apply current best practices (which is bcftools mpileup followed by something I forgot, see bcftools manual for variant cal…
Answer: Analysis of intronic reads included scRNA-seq data
by
ATpoint
82k
By default in CellRanger (lets assume you have 10x data processed with it) intronic reads are included. What you get in your matrix.mtx fil…
Comment: How does gene length effect the number of reads mapped
by
i.sudbery
19k
The number of reads for a gene is almost exactly linearly proportional to the length of the gene. In paired-end sequencing, we generally co…
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
ATpoint
82k
Can you post your setup, so how many groups and their replication number? I can tell you by experience that you need even more replication …
Answer: DSEQ2 analysis
by
ATpoint
82k
The tool is called D**E**Seq2. Anyway, if your factor is `factor(conditions, levels = c("control", "mutant"))` then the first level is the …
Comment: Odd alignment question/finding
by
barslmn
★ 2.1k
Maybe it is caused by fastp. https://github.com/OpenGene/fastp/issues/506
Comment: Generating mpileup file using samtools
by
Joe
21k
It's been a long time since I did this sort of thing, but I have a vague recollection that the mpileup process was made simpler and/or roll…
Comment: Introduce SNPs on FASTA
by
Riccardo
▴ 10
Thank you very much for your answer!
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This is great also for multiline fastas
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